We propose the dissection the function of [unreadable] Genes and genetic variants discovered in Crohn's disease (CD) using systems approaches. [unreadable] Recent linkage and association studies of CD have conclusively identified a number of genetic risk factors including CARD15, IBD5, IL23R, ATG16L1, IRGM, MST1 and NKX2.3. Among the novel genetic discoveries, ATG16L1 and IRGM are central regulators of autophagy, identifying a key [unreadable] role in disease pathogenesis for this previously unsuspected pathway. As part of the [unreadable] preliminary studies for this proposal we have demonstrated that ATG16L1 is essential [unreadable] for Classical and Salmonella induced autophagy. We also demonstrate that a 20- [unreadable] kilobase insertion/deletion polymorphism upstream of IRGM is associated with altered [unreadable] IRGM expression and is tightly linked to CD associated SNPs. These findings provide [unreadable] the first example of a structural variant influencing disease risk via expression of a [unreadable] nearby gene. We will integrate all available GWAS data, discover specifically causal [unreadable] coding and regulatory variants via high throughput sequencing, define the impact of [unreadable] these variants on gene expression (locally and globally), and assemble the set of [unreadable] variants into a systems level model involving potential genetic interactions on their [unreadable] influence on risk or gene expression. Given the involvement of two genes central to the [unreadable] autophagy response, we propose to apply systems approaches, synthetic biology and [unreadable] unique genetic tools to dissect mechanisms involved in the pathogenesis of CD. This [unreadable] proposal probes the function or consequences of, and pathways that interact with, [unreadable] human mutations that have been validated as playing a causal role in Crohn's disease. [unreadable] [unreadable] The broad goals of this proposal will pursued through studies of three specific aims: [unreadable] Aim 1: To define specific variants associated with Crohn's disease suitable for functional analysis. [unreadable] Aim 2: To identify small molecules that cause different cellular effects in epithelial cells and lymphoblastoid cells bearing mutations that are implicated in Crohn's disease. [unreadable] Aim 3: To delineate proteins required for ATG16L1 and IRGM autophagy response to bacteria using RNAi loss of function analysis [unreadable] [unreadable] [unreadable]